| | | | | | | requested parallelism | walltime sum (s) | nb instances | any sync average per thread time (s) | any wait average per thread time (s) | parallelism overhead (%) | local speedup if perfectly balanced | global speedup if perfectly balanced |
|---|
| start addr | function name | source location | level | ancestor thread num | invoker | parallel or teams | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 | 1x52 |
|---|
| libgromacs_mpi.so.7:0x62d1dc | _INTERNALce49b591::nbnxn_kernel_cpu(PairlistSet const&, Nbnx... | kerneldispatch.cpp:265 | 0 | 0 | runtime | parallel | 52 | 19.698 | 10.0 E3 | 1.377 | 1.375 | 6.99 | 1.075 | 1.026 |
| libgromacs_mpi.so.7:0xd1382e | gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<gmx::BasicVector<float>... | pme.cpp:1296 | 0 | 0 | runtime | parallel | 52 | 9.792 | 10.0 E3 | 1.635 | 1.625 | 16.7 | 1.200 | 1.031 |
| libgromacs_mpi.so.7:0xd35286 | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:936 | 0 | 0 | runtime | parallel | 52 | 3.752 | 10.0 E3 | 0.995 | 0.994 | 26.5 | 1.361 | 1.018 |
| libgromacs_mpi.so.7:0xd139bb | gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<gmx::BasicVector<float>... | pme.cpp:1401 | 0 | 0 | runtime | parallel | 52 | 2.433 | 10.0 E3 | 0.819 | 0.818 | 33.6 | 1.507 | 1.015 |
| libgromacs_mpi.so.7:0xc05577 | gmx::constrain_lincs(bool, t_inputrec const&, long, gmx::Lin... | lincs.cpp:2483 | 0 | 0 | runtime | parallel | 52 | 2.355 | 10.0 E3 | 0.957 | 0.918 | 40.6 | 1.685 | 1.018 |
| libgromacs_mpi.so.7:0xd353ae | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:1010 | 0 | 0 | runtime | parallel | 52 | 1.892 | 10.0 E3 | 0.459 | 0.458 | 24.3 | 1.321 | 1.008 |
| libgromacs_mpi.so.7:0xd023db | _INTERNAL115a3b1f::calcBondedForces(InteractionDefinitions c... | listed_forces.cpp:385 | 0 | 0 | runtime | parallel | 52 | 1.621 | 10.0 E3 | 0.300 | 0.299 | 18.5 | 1.228 | 1.005 |
| libgromacs_mpi.so.7:0xd40124 | fft5d_plan_3d(int, int, int, ompi_communicator_t**, int, t_c... | fft5d.cpp:643 | 0 | 0 | runtime | parallel | 52 | 1.213 | 6.00 | 55.7 E-3 | 55.7 E-3 | 4.59 | 1.048 | 1.001 |
| libgromacs_mpi.so.7:0x5fb2ff | _INTERNAL95fec573::nbnxn_atomdata_add_nbat_f_to_f_reduce(nbn... | atomdata.cpp:1188 | 0 | 0 | runtime | parallel | 52 | 1.208 | 10.0 E3 | 0.302 | 0.300 | 25.0 | 1.333 | 1.005 |
| libgromacs_mpi.so.7:0xd351ad | spread_on_grid(gmx_pme_t const*, PmeAtomComm*, pmegrids_t co... | pme_spread.cpp:910 | 0 | 0 | runtime | parallel | 52 | 1.052 | 10.0 E3 | 0.179 | 0.178 | 17.0 | 1.204 | 1.003 |
| libgromacs_mpi.so.7:0x5f9118 | nbnxn_atomdata_copy_x_to_nbat_x(Nbnxm::GridSet const&, gmx::... | atomdata.cpp:993 | 0 | 0 | runtime | parallel | 52 | 0.733 | 9.88 E3 | 0.342 | 0.341 | 46.7 | 1.875 | 1.006 |
| libgromacs_mpi.so.7:0xbda44d | L__ZN3gmx11Constraints4Impl5applyEbblifNS_19ArrayRefWithPadd... | constr.cpp:587 | 0 | 0 | runtime | parallel | 52 | 0.712 | 10.0 E3 | 0.194 | 0.192 | 27.2 | 1.373 | 1.004 |
| libgromacs_mpi.so.7:0x71e829 | PairlistSet::constructPairlists(gmx::InteractionLocality, Nb... | pairlist.cpp:3958 | 0 | 0 | runtime | parallel | 52 | 0.488 | 126 | 48.5 E-3 | 48.5 E-3 | 9.94 | 1.110 | 1.001 |
| libgromacs_mpi.so.7:0x7d1bff | void _INTERNALd56b7fc3::gmx::(anonymous namespace)::reduceTh... | threaded_force_buffer.cpp:170 | 0 | 0 | runtime | parallel | 52 | 0.434 | 10.0 E3 | 0.182 | 0.181 | 42.0 | 1.723 | 1.003 |
| libgromacs_mpi.so.7:0xc4dddb | gmx::Update::Impl::finish_update(t_inputrec const&, bool, in... | update.cpp:1637 | 0 | 0 | runtime | parallel | 52 | 0.401 | 10.0 E3 | 83.5 E-3 | 82.5 E-3 | 20.8 | 1.263 | 1.002 |
| libgromacs_mpi.so.7:0x73631f | PairlistSet::dispatchPruneKernel(nbnxn_atomdata_t const*, gm... | prunekerneldispatch.cpp:68 | 0 | 0 | runtime | parallel | 52 | 0.349 | 876 | 23.7 E-3 | 23.6 E-3 | 6.78 | 1.073 | 1.000 |
| libgromacs_mpi.so.7:0xc41858 | gmx::Update::Impl::update_coords(t_inputrec const&, long, in... | update.cpp:1687 | 0 | 0 | runtime | parallel | 52 | 0.339 | 10.0 E3 | 89.1 E-3 | 87.9 E-3 | 26.3 | 1.356 | 1.002 |
| libgromacs_mpi.so.7:0x76f2c4 | dd_make_local_constraints(gmx_domdec_t*, int, gmx_mtop_t con... | domdec_constraints.cpp:458 | 0 | 0 | runtime | parallel | 52 | 0.256 | 127 | 0.241 | 0.241 | 94.2 | 17.216 | 1.004 |
| libgromacs_mpi.so.7:0xc3686b | _INTERNAL14e05f89::setupForceOutputs(ForceHelperBuffers*, gm... | sim_util.cpp:473 | 0 | 0 | runtime | parallel | 52 | 0.135 | 10.0 E3 | 43.8 E-3 | 42.9 E-3 | 32.6 | 1.483 | 1.001 |
| libgromacs_mpi.so.7:0x5fad00 | reduceForces(nbnxn_atomdata_t*, gmx::AtomLocality, Nbnxm::Gr... | atomdata.cpp:1262 | 0 | 0 | runtime | parallel | 52 | 0.113 | 10.0 E3 | 26.5 E-3 | 25.5 E-3 | 23.4 | 1.305 | 1.000 |
| libgromacs_mpi.so.7:0xd2055f | unwrap_periodic_pmegrid(gmx_pme_t*, float*) | pme_grid.cpp:529 | 0 | 0 | runtime | parallel | 52 | 0.104 | 10.0 E3 | 52.3 E-3 | 51.3 E-3 | 50.0 | 2.002 | 1.001 |
| libgromacs_mpi.so.7:0xd20c53 | unwrap_periodic_pmegrid(gmx_pme_t*, float*) | pme_grid.cpp:512 | 0 | 0 | runtime | parallel | 52 | 85.8 E-3 | 10.0 E3 | 28.8 E-3 | 27.8 E-3 | 33.6 | 1.506 | 1.001 |
| libgromacs_mpi.so.7:0x7811a5 | _INTERNALd64f4cfb::make_local_bondeds_excls(gmx_domdec_t con... | localtopology.cpp:845 | 0 | 0 | runtime | parallel | 52 | 84.8 E-3 | 127 | 31.8 E-3 | 31.8 E-3 | 37.5 | 1.599 | 1.001 |
| libgromacs_mpi.so.7:0xd031ea | setup_bonded_threading(bonded_threading_t*, int, bool, Inter... | manage_threading.cpp:396 | 0 | 0 | runtime | parallel | 52 | 73.4 E-3 | 127 | 5.58 E-3 | 5.55 E-3 | 7.60 | 1.082 | 1.000 |
| libgromacs_mpi.so.7:0xc0fdf7 | _INTERNAL7742301e::calc_ke_part_normal(gmx::ArrayRef<gmx::Ba... | md_support.cpp:113 | 0 | 0 | runtime | parallel | 52 | 38.6 E-3 | 2.00 E3 | 4.98 E-3 | 4.80 E-3 | 12.9 | 1.148 | 1.000 |
| libgromacs_mpi.so.7:0x62428d | Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, g... | grid.cpp:1481 | 0 | 0 | runtime | parallel | 52 | 37.3 E-3 | 127 | 16.0 E-3 | 16.0 E-3 | 42.9 | 1.752 | 1.000 |
| libgromacs_mpi.so.7:0x72c31e | _INTERNALb629d8fd::rebalanceSimpleLists(gmx::ArrayRef<NbnxnP... | pairlist.cpp:3681 | 0 | 0 | runtime | parallel | 52 | 30.2 E-3 | 126 | 9.50 E-3 | 9.49 E-3 | 31.5 | 1.459 | 1.000 |
| libgromacs_mpi.so.7:0xc358ac | _INTERNAL14e05f89::postProcessForces(t_commrec const*, long,... | sim_util.cpp:149 | 0 | 0 | runtime | parallel | 52 | 20.8 E-3 | 1.00 E3 | 5.12 E-3 | 5.02 E-3 | 24.6 | 1.327 | 1.000 |
| libgromacs_mpi.so.7:0xc36ac8 | _INTERNAL14e05f89::setupForceOutputs(ForceHelperBuffers*, gm... | sim_util.cpp:473 | 0 | 0 | runtime | parallel | 52 | 19.3 E-3 | 1.00 E3 | 5.53 E-3 | 5.43 E-3 | 28.6 | 1.401 | 1.000 |
| libgromacs_mpi.so.7:0xbd4038 | calc_vir(int, float const (*) [3], float const (*) [3], floa... | calcvir.cpp:109 | 0 | 0 | runtime | parallel | 52 | 18.4 E-3 | 1.00 E3 | 2.39 E-3 | 2.30 E-3 | 13.0 | 1.149 | 1.000 |
| libgromacs_mpi.so.7:0xc11419 | atoms2md(gmx_mtop_t const&, t_inputrec const&, int, gmx::Arr... | mdatoms.cpp:327 | 0 | 0 | runtime | parallel | 52 | 15.4 E-3 | 127 | 2.41 E-3 | 2.39 E-3 | 15.6 | 1.185 | 1.000 |
| libgromacs_mpi.so.7:0xc0cb70 | gmx::set_lincs(InteractionDefinitions const&, int, gmx::Arra... | lincs.cpp:2196 | 0 | 0 | runtime | parallel | 52 | 13.3 E-3 | 127 | 2.07 E-3 | 2.05 E-3 | 15.6 | 1.184 | 1.000 |
| libgromacs_mpi.so.7:0xc0aad1 | _INTERNAL661916bb::gmx::lincs_thread_setup(_INTERNAL661916bb... | lincs.cpp:1636 | 0 | 0 | runtime | parallel | 52 | 11.6 E-3 | 127 | 1.59 E-3 | 1.57 E-3 | 13.7 | 1.159 | 1.000 |
| libgromacs_mpi.so.7:0xc09f40 | _INTERNAL661916bb::gmx::set_lincs_matrix(_INTERNAL661916bb::... | lincs.cpp:1347 | 0 | 0 | runtime | parallel | 52 | 6.46 E-3 | 127 | 1.99 E-3 | 1.91 E-3 | 30.8 | 1.445 | 1.000 |
| libgromacs_mpi.so.7:0x798c52 | dd_redistribute_cg(_IO_FILE*, long, gmx_domdec_t*, int*, t_s... | redistribute.cpp:624 | 0 | 0 | runtime | parallel | 52 | 5.00 E-3 | 126 | 479 E-6 | 467 E-6 | 9.59 | 1.106 | 1.000 |
| libgromacs_mpi.so.7:0xc0af66 | _INTERNAL661916bb::gmx::lincs_thread_setup(_INTERNAL661916bb... | lincs.cpp:1695 | 0 | 0 | runtime | parallel | 52 | 4.65 E-3 | 127 | 957 E-6 | 936 E-6 | 20.6 | 1.259 | 1.000 |
| libgromacs_mpi.so.7:0x62a5ae | Nbnxm::GridSet::putOnGrid(float const (*) [3], int, float co... | gridset.cpp:212 | 0 | 0 | runtime | parallel | 52 | 4.45 E-3 | 127 | 1.42 E-3 | 1.41 E-3 | 31.9 | 1.468 | 1.000 |
| libgromacs_mpi.so.7:0xda0ea6 | gmx_set_thread_affinity(gmx::MDLogger const&, t_commrec cons... | threadaffinity.cpp:314 | 0 | 0 | runtime | parallel | 52 | 4.16 E-3 | 1.00 | 140 E-6 | 104 E-6 | 3.36 | 1.035 | 1.000 |
| libgromacs_mpi.so.7:0xc5ba48 | _INTERNAL30ba3db8::do_stopcm_grp(t_mdatoms const&, gmx::Arra... | vcm.cpp:374 | 0 | 0 | runtime | parallel | 52 | 1.78 E-3 | 102 | 742 E-6 | 697 E-6 | 41.6 | 1.712 | 1.000 |
| libgromacs_mpi.so.7:0xc57b12 | calc_vcm_grp(t_mdatoms const&, gmx::ArrayRef<gmx::BasicVecto... | vcm.cpp:170 | 0 | 0 | runtime | parallel | 52 | 1.30 E-3 | 102 | 503 E-6 | 454 E-6 | 38.7 | 1.632 | 1.000 |
| libgromacs_mpi.so.7:0x7d743b | gmx::ThreadedForceBuffer<float [4]>::ThreadedForceBuffer(int... | threaded_force_buffer.cpp:230 | 0 | 0 | runtime | parallel | 52 | 46.5 E-6 | 1.00 | 15.1 E-6 | 15.0 E-6 | 32.6 | 1.483 | 1.000 |
| libgromacs_mpi.so.7:0xd34a76 | pme_init_all_work(pme_solve_work_t**, int, int) | pme_solve.cpp:144 | 0 | 0 | runtime | parallel | 52 | 39.4 E-6 | 1.00 | 23.5 E-6 | 23.4 E-6 | 59.6 | 2.477 | 1.000 |
| libgromacs_mpi.so.7:0x7bd2f9 | gmx_ekindata_t::gmx_ekindata_t(int, float, int) | group.cpp:66 | 0 | 0 | runtime | parallel | 52 | 7.97 E-6 | 1.00 | 3.30 E-6 | 3.14 E-6 | 41.4 | 1.706 | 1.000 |
| libgromacs_mpi.so.7:0xd174ff | PmeAtomComm::PmeAtomComm(ompi_communicator_t*, int, int, int... | pme.cpp:325 | 0 | 0 | runtime | parallel | 52 | 7.96 E-6 | 1.00 | 2.45 E-6 | 2.32 E-6 | 30.8 | 1.445 | 1.000 |
